Add CMakeLists.txt from feature/ufs of fv3-bundle and extend for SOCA…

.gitignore

@@ -1,11 +1,61 @@
-CMakeLists.txt.user
-CMakeCache.txt
-CMakeFiles
-CMakeScripts
-Testing
-Makefile
-cmake_install.cmake
-install_manifest.txt
-compile_commands.json
-CTestTestfile.cmake
-_deps
+# Ignore these files anywhere in the tree
+*DS_Store*
+*.[aox]
+*.so
+*.mod
+*.pyc
+*.v3breakpoints
+*.swp
+*.sublime-workspace
+*~
+git_branches_as_of_*
+
+# Ignore the contents of these directories
+build*/
+
+# ECMWF libraries
+atlas/
+eckit/
+fckit/
+
+
+# JEDI core repos
+jedicmake/
+saber/
+odc/
+odyssey/
+ioda-converters/
+ioda/
+oops/
+ufo/
+ewok/
+
+# FMS
+fms/
+
+# UFS
+ufs/
+
+# fv3-jedi and related repos
+fv3/
+femps/
+fv3-jedi-lm/
+fv3-jedi/
+
+# Observation operators
+crtm/
+gsw/
+geos-aero/
+ropp-ufo/
+
+# Test data
+fv3-jedi-data/
+test-data-release/
+ioda-data/
+ufo-data/
+saber-data/
+
+
+Testing/
+
+EWOK_TMP/

CMakeLists.txt

@@ -0,0 +1,186 @@
+# (C) Copyright 2021-2021 NOAA
+
+# ##########
+# ufs-jedi-bundle
+# ##########
+
+cmake_minimum_required( VERSION 3.12 FATAL_ERROR )
+
+find_package( ecbuild 3.5 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/../ecbuild)
+
+project( ufs-jedi-bundle VERSION 1.1.0 LANGUAGES C CXX Fortran )
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+
+include( ecbuild_bundle )
+
+set(DEPEND_LIB_ROOT ${CMAKE_CURRENT_BINARY_DIR}/Depends)
+list(APPEND CMAKE_PREFIX_PATH ${DEPEND_LIB_ROOT})
+message("prefix path is ${CMAKE_PREFIX_PATH}")
+
+# Default release mode
+set( ECBUILD_DEFAULT_BUILD_TYPE Release )
+
+# Enable MPI
+set( ENABLE_MPI ON CACHE BOOL "Compile with MPI")
+
+# Initialize
+ecbuild_bundle_initialize()
+ecbuild_bundle( PROJECT jedicmake GIT "https://github.com/jcsda-internal/jedi-cmake.git" BRANCH develop UPDATE )
+include( jedicmake/cmake/Functions/git_functions.cmake  )
+
+# ECMWF libs
+# ----------
+option("BUNDLE_SKIP_ECKIT" "Don't build eckit" "ON" ) # Skip eckit build unless user passes -DBUNDLE_SKIP_ECKIT=OFF
+option("BUNDLE_SKIP_FCKIT" "Don't build fckit" "ON") # Skip fckit build unless user passes -DBUNDLE_SKIP_FCKIT=OFF
+option("BUNDLE_SKIP_ATLAS" "Don't build atlas" "ON") # Skip atlas build unless user passes -DBUNDLE_SKIP_ATLAS=OFF
+
+ecbuild_bundle( PROJECT eckit GIT "https://github.com/ecmwf/eckit.git" TAG 1.16.0 )
+ecbuild_bundle( PROJECT fckit GIT "https://github.com/ecmwf/fckit.git" TAG 0.9.2 )
+ecbuild_bundle( PROJECT atlas GIT "https://github.com/ecmwf/atlas.git" TAG 0.24.1 )
+
+# External (required) observation operators
+# ------------------------------
+option("BUNDLE_SKIP_CRTM" "Don't build CRTM" "OFF") # Build crtm unless user passes -DBUNDLE_SKIP_CRTM=ON
+ecbuild_bundle( PROJECT crtm GIT "https://github.com/jcsda-internal/crtm.git" BRANCH release/crtm_jedi UPDATE )
+
+# Core JEDI repositories
+# ----------------------
+ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda-internal/oops.git"  BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda-internal/saber.git" BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda-internal/ioda.git"  BRANCH develop UPDATE )
+ecbuild_bundle( PROJECT ufo   GIT "https://github.com/jcsda-internal/ufo.git"   BRANCH develop UPDATE )
+
+# Options for building with certain models
+# ----------------------------------------
+set(UFS_APP "ATM" CACHE STRING "Choose the UFS Application")
+set_property(CACHE UFS_APP PROPERTY STRINGS "ATM" "NG-GODAS" "S2S")
+if(NOT UFS_APP MATCHES "^(ATM|NG-GODAS|S2S)$")
+  ecbuild_error("Valid options for -DUFS_APP are ATM|NG-GODAS|S2S")
+endif()
+ecbuild_info("Building with UFS application: ${UFS_APP}")
+
+# fv3-jedi linear model
+# ---------------------
+ecbuild_bundle( PROJECT fv3-jedi-lm GIT "https://github.com/jcsda-internal/fv3-jedi-linearmodel.git" BRANCH feature/ufs UPDATE )
+
+include_directories(${DEPEND_LIB_ROOT}/include)
+link_directories(${DEPEND_LIB_ROOT}/lib)
+
+include( ExternalProject )
+
+ExternalProject_Add(ufs-weather-model
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ufs-weather-model
+  GIT_REPOSITORY https://github.com/mark-a-potts/ufs-weather-model.git
+  GIT_SUBMODULES_RECURSE TRUE
+  GIT_TAG develop
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ufs-weather-model
+  INSTALL_DIR ${DEPEND_LIB_ROOT}
+  CMAKE_ARGS ${UFS_WEATHER_MODEL_ARGS}
+  CMAKE_ARGS -DCCPP_SUITES=FV3_GFS_v16,FV3_GFS_v16_coupled,FV3_GFS_v15p2 -DREPRO=on -DOPENMP=ON -DINLINE_POST=OFF -DMULTI_GASES=OFF -DMPI=ON -DAPP=ATM -DCMAKE_INSTALL_PREFIX=${DEPEND_LIB_ROOT}
+  INSTALL_COMMAND make install
+  BUILD_ALWAYS FALSE
+  )
+
+ExternalProject_Add(FMS
+  PREFIX ${CMAKE_CURRENT_BINARY_DIR}/fms
+  GIT_REPOSITORY https://github.com/jcsda/FMS.git
+  GIT_SUBMODULES_RECURSE TRUE
+  GIT_TAG dev/jcsda
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/fms
+  INSTALL_DIR ${DEPEND_LIB_ROOT}
+  CMAKE_ARGS -DGFS_PHYS=ON -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_Fortran_FLAGS="-fPIC" -D64BIT=ON -DOPENMP=ON -DCMAKE_INSTALL_PREFIX=${DEPEND_LIB_ROOT}
+  INSTALL_COMMAND make install
+  BUILD_ALWAYS TRUE
+  )
+
+add_dependencies(ufs-weather-model FMS )
+add_library( ufs IMPORTED STATIC)
+add_library( FMS::fms_r4 IMPORTED STATIC)
+add_library( FMS::fms_r8 IMPORTED STATIC)
+add_library( ccpp IMPORTED STATIC)
+add_library( stochastic_physics IMPORTED STATIC)
+add_library( fv3atm IMPORTED STATIC)
+add_library( ccppphys IMPORTED STATIC)
+set_target_properties(FMS::fms_r4 PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libfms_r4.a)
+set_target_properties(FMS::fms_r8 PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libfms_r8.a)
+set_target_properties(ufs PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libufs.a)
+set_target_properties(ccpp PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libccpp_framework.a)
+set_target_properties(stochastic_physics PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libstochastic_physics.a)
+set_target_properties(fv3atm PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libfv3atm.a)
+set_target_properties(ccppphys PROPERTIES IMPORTED_LOCATION ${DEPEND_LIB_ROOT}/lib/libccpp_physics.a)
+
+if(UFS_APP MATCHES "^(S2S)$")
+  # fv3-jedi and associated repositories
+  # ------------------------------------
+  ecbuild_bundle( PROJECT femps    GIT "https://github.com/jcsda-internal/femps.git"    BRANCH develop UPDATE )
+  ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs UPDATE )
+  ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git"     BRANCH develop UPDATE )
+  ecbuild_bundle( PROJECT soca     GIT "https://github.com/jcsda-internal/soca.git"     BRANCH develop UPDATE )
+elseif(UFS_APP MATCHES "^(NG-GODAS)$")
+  ecbuild_bundle( PROJECT gsw GIT "https://github.com/jcsda-internal/GSW-Fortran.git"     BRANCH develop UPDATE )
+  ecbuild_bundle( PROJECT soca     GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs UPDATE )
+elseif(UFS_APP MATCHES "^(ATM)$")
+  ecbuild_bundle( PROJECT femps    GIT "https://github.com/jcsda-internal/femps.git"    BRANCH develop UPDATE )
+  ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs UPDATE )
+endif()
+
+
+# ioda, ufo, fv3-jedi and saber test data
+#----------------------------------------
+
+# If IODA branch is being built set GIT_BRANCH_FUNC to IODA's current branch.
+# If a tagged version of IODA is being built set GIT_TAG_FUNC to ioda's current tag. In this case,
+# IODA test files will be download from UCAR DASH and ioda-data repo will not be cloned.
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+
+find_branch_name(REPO_DIR_NAME ioda)
+# When LOCAL_PATH_JEDI_TESTFILES is set to the directory of IODA test files stored
+# in a local directory, ioda-data repo will not be cloned
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT ioda-data GIT "https://github.com/JCSDA-internal/ioda-data.git" BRANCH develop UPDATE )
+endif()
+
+# If IODA's current branch is available in ioda-data repo, that branch will be checked out
+branch_checkout (REPO_DIR_NAME ioda-data
+                 BRANCH ${GIT_BRANCH_FUNC} )
+
+# same procedure for ufo-data
+find_branch_name(REPO_DIR_NAME ufo)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT ufo-data GIT "https://github.com/JCSDA-internal/ufo-data.git" BRANCH develop UPDATE )
+endif()
+
+# If UFO's current branch is available in ufo-data repo, that branch will be checked out
+branch_checkout (REPO_DIR_NAME ufo-data
+                 BRANCH ${GIT_BRANCH_FUNC} )
+
+# same procedure for fv3-jedi-data
+find_branch_name(REPO_DIR_NAME fv3-jedi)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH develop UPDATE )
+endif()
+
+# If fv3-jedi's current branch is available in fv3-jedi-data repo, that branch will be checked out
+branch_checkout (REPO_DIR_NAME fv3-jedi-data
+                 BRANCH ${GIT_BRANCH_FUNC} )
+
+# same procedure for saber-data
+find_branch_name(REPO_DIR_NAME saber)
+if( NOT DEFINED ENV{LOCAL_PATH_JEDI_TESTFILES} AND NOT DEFINED ${GIT_TAG_FUNC} )
+  ecbuild_bundle( PROJECT saber-data GIT "https://github.com/JCSDA-internal/saber-data.git" BRANCH develop UPDATE )
+endif()
+
+# If saber's current branch is available in saber-data repo, that branch will be checked out
+branch_checkout (REPO_DIR_NAME saber-data
+                 BRANCH ${GIT_BRANCH_FUNC} )
+
+# Build Doxygen documentation
+# ---------------------------
+option(BUILD_UFSJEDI_BUNDLE_DOC "Build documentation" OFF)
+if(BUILD_UFSJEDI_BUNDLE_DOC)
+   add_subdirectory( Documentation )
+endif()
+
+ecbuild_bundle_finalize()

README.md

@@ -1,2 +1,2 @@
-# ufsjedi-bundle
+# ufs-jedi-bundle
 Bundle for interfacing UFS models with JEDI interfaces